A new discovery has pushed the timeline of the plague in Europe back even earlier than we had previously thought. A new strain of the Yersinia pestis bacterium has been identified in 4,900-year-old bones in a Neolithic burial site in Sweden.

It’s the oldest strain ever identified, and the most basal we’ve seen – that is, the closest strain to the genetic origin of the bacterium.

Y. pestis has been an absolute blight on humanity throughout history, repeatedly wiping out vast swathes of the population.

It was responsible for the Plague of Justinian that broke out 541 CE, ultimately killing 25-50 million people; the Black Death of the 14th century, which wiped out 75 to 200 million people across Eurasia; the Great Plague of London of 1665-1666 CE, which killed 100,000 people, nearly a quarter of the city’s population, in just 18 months; and the Third Pandemic, which broke out in 1855 and killed 12 million people in India and China.

“Plague is maybe one of the deadliest bacteria that has ever existed for humans,” said geneticist Simon Rasmussen of the Technical University of Denmark and the University of Copenhagen.

“The kind of analyses we do here let us go back through time and look at how this pathogen that’s had such a huge effect on us evolved.”

The discovery of Y. pestis in the bones of a 20-year-old Neolithic woman suggests the plague spread across Europe much earlier than previously thought, according to the new research.

But if the bacteria spread across Europe earlier, that could help explain a mystery that has long perplexed scientists – namely, the disappearance of the early European farmers.

These were people who had migrated from the Middle East starting around 9,000 years ago, and they congregated in settlements of up to 20,000 people. These people – called the Trypillia Culture – developed technology, such as pottery, the wheel and metallurgy, and they kept livestock.

But around 5,400 years ago, they just… disappeared. Their settlements stopped being built, and there was a drastic change in the genome starting about 4,500 years ago, suggesting a new influx of people from the steppe, which eventually replaced the Trypillia Culture.

So what happened to the Trypillians? It’s a baffling mystery with many potential explanations that have been hotly debated. Perhaps they merely assimilated into other incoming cultures. Perhaps they were conquered. Perhaps their resources ran out and they had to move on.

But Rasmussen and his team believe it could have been something else. The strain of Y. pestis they found in Sweden diverged from the other strains around 5,700 years ago – before the influx of steppe populations.

Those huge Trypillian settlements, with no proper sanitation, and with humans living in close quarters with animals, could have been amazing breeding grounds for pathogens. The plague could have evolved right there in those European settlements.

“We think our data fit. If plague evolved in the mega-settlements, then when people started dying from it, the settlements would have been abandoned and destroyed,” Rasmussen said.

“This is exactly what was observed in these settlements after 5,500 years ago. Plague would also have started migrating along all the trade routes made possible by wheeled transport, which had rapidly expanded throughout Europe in this period.”

And those trade routes are how the plague could have ended up in Sweden 4,900 years ago.

But at this point, these hypotheses are far from definitive, particularly because Y. pestis has not yet been identified in any Trypillian remains or settlement sites. That’s the next step in the research.

“We haven’t really found the smoking gun, but it’s partly because we haven’t looked yet,” Rasmussen said. “And we’d really like to do that, because if we could find plague in those settlements, that would be strong support for this theory.”